Phylogenetic Analysis of IAP Proteins
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Corresponding Organization : Medical College of Wisconsin
Protocol cited in 11 other protocols
Variable analysis
- Sequences obtained for human (h) Survivin (Uniprot O15392), Bruce (Q9NR09), cIAP1 (Q13490), cIAP2 (Q13489), XIAP (P98170), ILP2 (Q96P09), MLIAP (Q96CA5), and NAIP (Q13075) with the individual BIR domains parsed
- XIAP sequences for Drosophila (d, I6L9G1), Gallus (c, F6TJT0), Xenopus (x, A5D8Q0), Mus (m, Q60989), and Rattus (r, Q9R0I6)
- Sequence alignments performed using Clustal Omega
- Phylogenetic analysis of the domains using maximum likelihood with the JTT matrix and a consensus of 1000 bootstrap replicates using MEGA5
- Variants of XIAP associated with disease identified in published literature, utilizing only single amino acid changes (including mutations to stop codons (X) and not mutations that result in a frameshift)
- Default settings used for Clustal Omega
- JTT matrix used for maximum likelihood analysis
- Neighbor-Join and BioNJ algorithms used to obtain initial tree for heuristic search
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